Something must have changed in focus handling in Java 1.6, because running RText in a 1.6 JRE causes a focus problem in the file chooser. In 1.5.x and older JRE's, there is no issue.
The problem is with the popup window displaying filename choices as you type a file to open in the file chooser. When using Java 1.6, that popup window can be made to not be "on top" of the main file chooser window. Once this happens, it is all but impossible to get it back on top where it belongs.
1. Open the file chooser, and type a directory name. Note the popup window offering you suggestions as you type.
2. Open any file; this causes the file chooser to close.
3. Re-open the file chooser. Start typing a new filename to open that includes subdirectories (e.g. "C:\windows\system32"). You'll note that sometime when you're typing, the popup suggestion window will "pop under" the main file chooser window, making it unusable. The popup will never again be above the file chooser.